Increasing use prevalence of waterpipe tobacco products raises concerns about environmental impacts from waterpipe waste disposal. The U.S. Food and Drug Administration (FDA) is required to assess the environmental impact of its tobacco regulatory actions per the National Environmental Policy Act. This study builds on FDA’s efforts characterizing the aquatic toxicity of waterpipe wastewater chemicals. We compiled a comprehensive list of waterpipe wastewater chemical concentrations from literature. We then selected chemicals for risk assessment by estimating persistence, bioaccumulation, and aquatic toxicity (PBT) characteristics (U.S. Environmental Protection Agency), and hazardous concentration values (concentration affecting specific proportion of species). Of 38 chemicals in waterpipe wastewater with concentration data, 20 are listed as harmful or potentially harmful constituents (HPHCs) in tobacco smoke and tobacco products by FDA, and 15 are hazardous waste per U. S. Environmental Protection Agency. Among metals, six (cadmium, chromium, lead, mercury, nickel and selenium) are included in both HPHC and hazardous waste lists and were selected for future risk assessments. Among non-metals, nicotine, and 4-methylnitrosamino-1-(3-pyridyl)− 1-butanone (NNK) were shortlisted, as they are classified as persistent and toxic. Further, N-nitrosonornicotine (NNN), with a low hazardous concentration value (HC50; concentration affecting 50 % of aquatic species) for chronic aquatic toxicity, had high aquatic toxicity concern and is selected. The presence of multiple hazardous compounds in waterpipe wastewater highlights the importance of awareness on the proper disposal of waterpipe wastewater in residential and retail settings. Future studies can build on the hazard characterization provided in this study through fate and transport modeling, exposure characterization and risk assessments of waterpipe wastewater chemicals. •First screening-level hazard characterization of waterpipe wastewater chemicals.•Selection of waterpipe wastewater chemicals for future ecological and human health risk assessments.•Highlights environmental and water quality concerns from hazardous chemicals in waterpipe wastewater.•Emphasizes importance of awareness on waterpipe waste disposal practices.•Advances FDA’s evaluation of the environmental impacts of waterpipe tobacco per U.S. National Environmental Policy Act.